so you just put a motor and a #3 rec in and now your getting the 1A cycling in and out problem eh?
Have you gone to flight systems and downloaded the EV1 manual and looked in there for pointers on what could be causing this problem?
There are several parts in the troubleshooting section that refer to PMT trip scenarios regarding the 1A circuit.

My guess is since you have a new motor in place it has changed the resistance in the drive circuit and you need to do a tuneup (which has already been half way done from your responses)
What you may need to do is do a full tune up using an amp meter and setting these trimpots according to your amp draw readings so you can get the 1A time and Dropout set correctly, also the CL (current limit). With this new motor all those values would have changed and the card needs to be retuned to the new motor.
Of course the contactor itself may be bouncing and by all means check it but there are other things that can cause the 1A to trip out like this and the PMT will kick the 1A out like that if there is an overcurrent situation or short being picked up by the card monitoring circuit.

There are other tests to consider also within this troubleshooting section as well.

correct the url by removing the spaces i added and get this manual and use it, i'm sure it will be very helpful
h t t p://w w w.fsip.biz/Documents/EV1.pdf